Remove pan from heat; add 3 cups of the Cheddar cheese, all of the Gruyère cheese, 1/2 tablespoon salt, pepper, and nutmeg. Stir until all of the cheese is melted and the sauce is creamy and smooth.
Add the cooked macaroni and stir well. Pour into a 3-quart baking dish.
Melt the remaining 2 tablespoons of butter; mix the Panko bread crumbs.
Top macaroni and cheese with remaining 1-1/2 cups Cheddar Cheese and Panko bread crumbs mixed with butter.
May be prepared in advance up to this point and refrigerated.